Soil Type Is the Primary Determinant of the Composition of the Total and Active Bacterial Communities in Arable Soils

ABSTRACT Degradation of agricultural land and the resulting loss of soil biodiversity and productivity are of great concern. Land-use management practices can be used to ameliorate such degradation. The soil bacterial communities at three separate arable farms in eastern England, with different farm management practices, were investigated by using a polyphasic approach combining traditional soil analyses, physiological analysis, and nucleic acid profiling. Organic farming did not necessarily result in elevated organic matter levels; instead, a strong association with increased nitrate availability was apparent. Ordination of the physiological (BIOLOG) data separated the soil bacterial communities into two clusters, determined by soil type. Denaturing gradient gel electrophoresis and terminal restriction fragment length polymorphism analyses of 16S ribosomal DNA identified three bacterial communities largely on the basis of soil type but with discrimination for pea cropping. Five fields from geographically distinct soils, with different cropping regimens, produced highly similar profiles. The active communities (16S rRNA) were further discriminated by farm location and, to some degree, by land-use practices. The results of this investigation indicated that soil type was the key factor determining bacterial community composition in these arable soils. Leguminous crops on particular soil types had a positive effect upon organic matter levels and resulted in small changes in the active bacterial population. The active population was therefore more indicative of short-term management changes.

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From pine to pasture: land use history has long-term impacts on soil bacterial community composition and functional potential

FEMS Microbiology Ecology ◽

10.1093/femsec/fiaa041 ◽

2020 ◽

Vol 96 (4) ◽

Author(s):

Syrie M Hermans ◽

Matthew Taylor ◽

Gwen Grelet ◽

Fiona Curran-Cournane ◽

Hannah L Buckley ◽

...

Keyword(s):

Land Use ◽

Bacterial Community ◽

Community Composition ◽

Bacterial Communities ◽

Bacterial Community Composition ◽

Reference Sites ◽

Functional Potential ◽

Soil Bacterial Communities ◽

Soil Bacterial

ABSTRACT Bacterial communities are crucial to soil ecosystems and are known to be sensitive to environmental changes. However, our understanding of how present-day soil bacterial communities remain impacted by historic land uses is limited; implications for their functional potential are especially understudied. Through 16S rRNA gene amplicon and shotgun metagenomic sequencing, we characterized the structure and functional potential of soil bacterial communities after land use conversion. Sites converted from pine plantations to dairy pasture were sampled five- and eight-years post conversion. The bacterial community composition and functional potential at these sites were compared to long-term dairy pastures and pine forest reference sites. Bacterial community composition and functional potential at the converted sites differed significantly from those at reference sites (P = 0.001). On average, they were more similar to those in the long-term dairy sites and showed gradual convergence (P = 0.001). Differences in composition and functional potential were most strongly related to nutrients such as nitrogen, Olsen P and the carbon to nitrogen ratio. Genes related to the cycling of nitrogen, especially denitrification, were underrepresented in converted sites compared to long-term pasture soils. Together, our study highlights the long-lasting impacts land use conversion can have on microbial communities, and the implications for future soil health and functioning.

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Changes in soil bacterial communities, and carbon and nitrogen metrics as potential indicators of land use effects in a humid tropical forest

Pedobiologia ◽

10.1016/j.pedobi.2021.150730 ◽

2021 ◽

Vol 85-86 ◽

pp. 150730

Author(s):

William D. Eaton ◽

Katie M. McGee ◽

Morgan Larimer ◽

Elizabeth Hoke ◽

Olivia Karas ◽

...

Keyword(s):

Land Use ◽

Tropical Forest ◽

Bacterial Communities ◽

Carbon And Nitrogen ◽

Soil Bacterial Communities ◽

Land Use Effects ◽

Humid Tropical Forest ◽

Soil Bacterial

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Pyrosequencing-Based Assessment of Soil pH as a Predictor of Soil Bacterial Community Structure at the Continental Scale

Applied and Environmental Microbiology ◽

10.1128/aem.00335-09 ◽

2009 ◽

Vol 75 (15) ◽

pp. 5111-5120 ◽

Cited By ~ 1989

Author(s):

Christian L. Lauber ◽

Micah Hamady ◽

Rob Knight ◽

Noah Fierer

Keyword(s):

Bacterial Community ◽

Soil Ph ◽

Bacterial Communities ◽

Bacterial Community Structure ◽

Spatial Scales ◽

Bacterial Community Composition ◽

Phylogenetic Structure ◽

Soil Bacterial Communities ◽

Soil Bacterial Community Structure ◽

Soil Bacterial

ABSTRACT Soils harbor enormously diverse bacterial populations, and soil bacterial communities can vary greatly in composition across space. However, our understanding of the specific changes in soil bacterial community structure that occur across larger spatial scales is limited because most previous work has focused on either surveying a relatively small number of soils in detail or analyzing a larger number of soils with techniques that provide little detail about the phylogenetic structure of the bacterial communities. Here we used a bar-coded pyrosequencing technique to characterize bacterial communities in 88 soils from across North and South America, obtaining an average of 1,501 sequences per soil. We found that overall bacterial community composition, as measured by pairwise UniFrac distances, was significantly correlated with differences in soil pH (r = 0.79), largely driven by changes in the relative abundances of Acidobacteria, Actinobacteria, and Bacteroidetes across the range of soil pHs. In addition, soil pH explains a significant portion of the variability associated with observed changes in the phylogenetic structure within each dominant lineage. The overall phylogenetic diversity of the bacterial communities was also correlated with soil pH (R2 = 0.50), with peak diversity in soils with near-neutral pHs. Together, these results suggest that the structure of soil bacterial communities is predictable, to some degree, across larger spatial scales, and the effect of soil pH on bacterial community composition is evident at even relatively coarse levels of taxonomic resolution.

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Soil characteristics more strongly influence soil bacterial communities than land-use type

FEMS Microbiology Ecology ◽

10.1111/j.1574-6941.2011.01192.x ◽

2011 ◽

Vol 79 (1) ◽

pp. 12-24 ◽

Cited By ~ 202

Author(s):

Eiko E. Kuramae ◽

Etienne Yergeau ◽

Lina C. Wong ◽

Agata S. Pijl ◽

Johannes A. Veen ◽

...

Keyword(s):

Land Use ◽

Bacterial Communities ◽

Soil Characteristics ◽

Land Use Type ◽

Soil Bacterial Communities ◽

Soil Bacterial

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Impact of Maize–Mushroom Intercropping on the Soil Bacterial Community Composition in Northeast China

Agronomy ◽

10.3390/agronomy10101526 ◽

2020 ◽

Vol 10 (10) ◽

pp. 1526

Author(s):

Xiaoqin Yang ◽

Yang Wang ◽

Luying Sun ◽

Xiaoning Qi ◽

Fengbin Song ◽

...

Keyword(s):

Bacterial Communities ◽

Northeast China ◽

Management Practice ◽

Bacterial Community Composition ◽

Soil Microbial Communities ◽

Chemical Properties ◽

Crop Productivity ◽

Rrna Gene ◽

Soil Bacterial Communities ◽

Soil Bacterial

Conservative agricultural practices have been adopted to improve soil quality and maintain crop productivity. An efficient intercropping of maize with mushroom has been developed in Northeast China. The objective of this study was to evaluate and compare the effects of planting patterns on the diversity and structure of the soil bacterial communities at a 0–20 cm depth in the black soil zone of Northeast China. The experiment consisted of monoculture of maize and mushroom, and intercropping in a split-plot arrangement. The characteristics of soil microbial communities were performed by 16S rRNA gene amplicom sequencing. The results showed that intercropping increased soil bacterial richness and diversity compared with maize monoculture. The relative abundances of Acidobacteria, Chloroflexi, Saccharibacteria and Planctomycetes were significantly higher, whereas Proteobacteria and Firmicutes were lower in intercropping than maize monoculture. Redundancy analysis suggested that pH, NO3−-N and NH4+-N contents had a notable effect on the structure of the bacterial communities. Moreover, intercropping significantly increased the relative abundance of carbohydrate metabolism pathway functional groups. Overall, these findings demonstrated that intercropping of maize with mushroom strongly impacts the physical and chemical properties of soil as well as the diversity and structure of the soil bacterial communities, suggesting this is a sustainable agricultural management practice in Northeast China.

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The Influence of Land Use Patterns on Soil Bacterial Community Structure in the Karst Graben Basin of Yunnan Province, China

Forests ◽

10.3390/f11010051 ◽

2019 ◽

Vol 11 (1) ◽

pp. 51 ◽

Cited By ~ 1

Author(s):

Jiangmei Qiu ◽

Jianhua Cao ◽

Gaoyong Lan ◽

Yueming Liang ◽

Hua Wang ◽

...

Keyword(s):

Land Use ◽

Surface Layer ◽

Bacterial Community ◽

Bacterial Communities ◽

Yunnan Province ◽

Soil Bacterial Community ◽

Land Use Patterns ◽

Use Patterns ◽

Soil Bacterial Communities ◽

Soil Bacterial

Land use patterns can change the structure of soil bacterial communities. However, there are few studies on the effects of land use patterns coupled with soil depth on soil bacterial communities in the karst graben basin of Yunnan province, China. Consequently, to reveal the structure of the soil bacterial community at different soil depths across land use changes in the graben basins of the Yunnan plateau, the relationship between soil bacterial communities and soil physicochemical properties was investigated for a given area containing woodland, shrubland, and grassland in Yunnan province by using next-generation sequencing technologies coupled with soil physicochemical analysis. Our results indicated that the total phosphorus (TP), available potassium (AK), exchangeable magnesium (E-Mg), and electrical conductivity (EC) in the grassland were significantly higher than those in the woodland and shrubland, yet the total nitrogen (TN) and soil organic carbon (SOC) in the woodland were higher than those in the shrubland and grassland. Proteobacteria, Verrucomicrobia, and Acidobacteria were the dominant bacteria, and their relative abundances were different in the three land use types. SOC, TN, and AK were the most important factors affecting soil bacterial communities. Land use exerts strong effects on the soil bacterial community structure in the soil’s surface layer, and the effects of land use attenuation decrease with soil depth. The nutrient content of the soil surface layer was higher than that of the deep layer, which was more suitable for the survival and reproduction of bacteria in the surface layer.

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